7ZB3

Crystal structure of beta-xylosidase from Thermotoga maritima in complex with xylohexaose hydrolysed to xylobiose

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7ZEQ	D_1292121589

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.9	293	3% polyethylene glycol 8000, 48% 2-methyl-2,4-pentanediol, 0.1 M sodium cacodylate pH 5.9

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 178.53	α = 90
b = 98.72	β = 90
c = 100.7	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	175	PIXEL	DECTRIS EIGER2 XE 16M		2021-11-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.51	87.71	100	1	56.5	13.4		259769

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.51	1.54			0.323

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	D_1292121589	1.51	87.709	259668	12762	93.495	0.168	0.1671	0.19	23.351

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-1.224			2.552		-1.328

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.306
r_dihedral_angle_4_deg	17.876
r_dihedral_angle_3_deg	12.53
r_dihedral_angle_1_deg	7.016
r_lrange_it	5.083
r_lrange_other	5.016
r_scangle_it	4.441
r_scangle_other	4.441
r_scbond_it	3.03
r_scbond_other	3.029
r_mcangle_it	2.2
r_mcangle_other	2.2
r_angle_refined_deg	1.673
r_mcbond_it	1.667
r_mcbond_other	1.667
r_angle_other_deg	1.472
r_nbd_refined	0.211
r_symmetry_nbd_other	0.177
r_nbtor_refined	0.169
r_nbd_other	0.139
r_symmetry_nbd_refined	0.138
r_xyhbond_nbd_refined	0.116
r_symmetry_xyhbond_nbd_refined	0.105
r_chiral_restr	0.086
r_symmetry_nbtor_other	0.08
r_ncsr_local_group_1	0.052
r_symmetry_xyhbond_nbd_other	0.04
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11867
Nucleic Acid Atoms
Solvent Atoms	1023
Heterogen Atoms	54

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing